Deposition
http://www.ebi.ac.uk/msd-srv/emdep
BIOCHEMICALSAMPLE
SPECIMENPREPARATION IMAGING
IMAGEPROCESSINGRECONSTRUCTION
MAP-FITTING
ELECTRONICNOTEBOOK
MICROSCOPEFILM/CCD
ELECTRONICNOTEBOOK
SCANSPARTICLE –
PICKING
3D RECON-STRUCTIONSOFTWARE
MAP FITTINGSOFTWARE
3DEM WORKFLOW PIPELINE
EM Data Collection
Structure AnalysisImage Processing
EM SpecimenPreparation
Biochemical Preparation
EM
em_assembly
_em_assembly.id
_em_assembly.entry_id
_em_assembly.name
_em_assembly.aggregation_state
_em_assembly.composition
_em_assembly.num_components
_em_assembly.mol_wt_exp
_em_assembly.mol_wt_theo
_em_assembly.mol_wt_method
_em_assembly.details
Biological Sample
Biological Sample
em_assembly
em_entity_assembly
em_entity_assembly_list
em_icos_virus_shells
em_virus_entity
Growth of EM Entries
Data filesData files
3D-EM map3D-EM map
MetadescriptorsMetadescriptors
Release: immediateTitle: “The Structure of the Semliki Forest Virus at 9 Å resolution”Authors: E. Mancini M. Clarke B. E. Gowen T. Rutten S. D. FullerReference paper: Mol Cell (2000) 5, 255Complex
Name: Semliki Forest Virus SFVAggregation: icosahedralDescribe composition: partial
ComponentsName:
spike glycoprotein E1spike glycoprotein E2spike glycoprotein E3coat protein C
Type: proteinSource: naturalSource organism: Semliki Forest Virus
ExperimentMicroscope: TEMTemperature range: liquid nitrogenReconstruction method: fourier-bessel
Mandatory
Optional
Database content
Figures
Slices
Masks
3D-EM Deposited Data
MANDATORY: 3D- EM MAPS
TEXTUAL DESCRIPTORS
OPTIONAL ADDITIONAL DATA FILES:
MASKS
SUPPLEMENTARY FIGURES
ORTHOGONAL MAP SLICES
STRUCTURE FACTORS
FSC .xml FILE
LAYER-LINE DATA
Biological Sample
Biochemical Preparation
EM Specimen Preparation
EM Data Collection
Image Processing
Structure Analysis
Textual Descriptors
EM Deposition
INTERACTIVE DEPOSITION SYSTEM:
13 DEPOSITION PAGES
120 DATA ITEMS
INFORMATION AND HELP ON PAGE
UPLOADED FILES
'BASED ON' FACILITY
Sample Details Page
XML data automatically
Filled in by software
Reading map headers
MAPS em2em – CCP4
EM Deposition Data
SINGLE PARTICLES ICOSAHEDRAL VIRUSES TOMOGRAPHY HELICAL ASSEMBLIES 2D-CRYSTALS
EM DATA FROM METHODOLOGIES INCLUDING:
Demonstration
Worldwide Protein Data Bankwww.wwpdb.org
Proposed Method for Depositing and Retrieving EM Data
IntegratedRCSB deposition
system
IntegratedMSD deposition
system
EB
IR
CS
B
map and fitted coordinateFTP repository
EM map/model assessment, visualization
and analysis tools
MSDDatabase
RCSBDatabase
Electron Microscopy Access Portal
Combined Dictionary for Map and Coordinate Data
Next slides only to be used if demo fails
Title author
Sample components
Sample components
Single Particle
Individual Structure (Tomogram)
2d/3d crystal
icosahedral
helical
TO FINALLY DEPOSIT THE ENTRY:
click on ‘GET ACCESSION NUMBER’ button (upper left).
You will receive by email an ‘ACCESSION’ number for your entry (eg EMD-1234) which can be used in EMsearch to link to the atlas pages for your entry.
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